The present invention relates to the determination of the complete DNA sequence of Ureaplasma urealyticum (Uu) and to the use of novel genes and sequences as probes and primers for assays for use in the detection and/or quantification of Uu in a sample.
Ureaplasma urealyticum (Uu) is a Mycoplasma which was first discovered in men with nongonococcal urethritis (NGU) in 1954. Approximately two-thirds of adults have Uu as part of their normal flora. Uu has been associated with and suspected as a pathogen in adverse pregnancy outcomes such as chorioamnionitis, intrauterine infection, and premature births. Uu has also been diagnosed as the causative agent of neonatal diseases such as pneumonia, meningitis, and sepsis. Uu has also been isolated in certain patients suffering from suppurative arthritis, especially those having hypogammaglobulinemia.
The primary mechanism of transmission of Uu is by sexual contact which can then be transmitted to neonates born to infected mothers.
The biology of Uu, which is a member of the Mycoplasma family, is unique. The Mycoplasma family is a family of wall-less bacteria which has descended from low G+C Gram positive bacteria. The Mycoplasma are included among the smallest free-living cells known. Additionally, the Mycoplasma use an alternate genetic code wherein the codon UGA=tryptophan (trp) rather than a stop or termination codon. Additionally, the Mycoplasma are biochemically different in that they possess no TCA cycle and most Mycoplasma require cholesterol for growth.
Ureaplasma urealyticum infections are commonly asymptomatic, it is important to have specific and sensitive methods for detecting their presence in a patient. Mycoplasmas including Ureaplasma urealyticum are somewhat atypical organisms and are difficult and are complex to culture. It is difficult for clinical laboratories to perform culture isolation of Mycoplasmas and consequently there are no relatively easy and inexpensive methods for diagnosing the presence of this bacterium.
Genetic probes and detection methods for detecting Mycoplasmas including Ureaplasma urealyticum have been developed. U.S. Pat. No. 5,843,667 to Weisburg et al. discloses various nucleic acid sequences which are capable of hybridizing to rRNA and rDNA of Mycoplasma etiological agents including Ureaplasma urealyticum. The nucleic acid probes disclosed in the Weisburg et al. patent specifically hybridize to 16S rRNA or 16S rDNA of Ureaplasma urealyticum. Similarly, U.S. Pat. No. 5,728,522 to Del Vecchio et al. discloses a method for detecting Ureaplasma urealyticum involving in vitro nucleic acid amplification by contacting Ureaplasma urealyticum target nucleic acids with an oligonucleotide fragment consisting of a contiguous nucleotide of Ureaplasma urealyticum DNA inserted into the plasmid pCU3900 having ATCC Accession No. 97424.
Neither U.S. Pat. No. 5,843,667 nor U.S. Pat. No. 5,728,522 disclose the entire DNA sequence of Ureaplasma urealyticum serovar 3 and, in fact, only disclose small DNA and/or RNA sequences from Ureaplasma urealyticum. 
Therefore, in order to better understand the nature and effects of Ureaplasma urealyticum, as well as to more accurately and consistently detect and diagnose the presence of Ureaplasma urealyticum in a potential carrier and to better develop antibiotic drugs specifically effective against Ureaplasma urealyticum, which, consequently, has no current antibiotic directed specifically against it, it would be advantageous to isolate and determine the gene sequences and functions which are unique to Ureaplasma urealyticum and utilize these sequences as a basis for detecting Ureaplasma urealyticum in a patient and thereby be able to more effectively treat those patients infected with Ureaplasma urealyticum as well as to develop new and improved drug therapies against Ureaplasma urealyticum. 
A method of detecting a nucleic acid sequence in Ureaplasma urealyticum serovar 3 includes the steps of isolating a specimen containing nucleic acid; and analyzing the specimen with an assay such as in situ hybridization, Southern blotting, single strand conformational polymorphism, restriction endonuclease fingerprinting (REF), PCR amplification, 5xe2x80x2 nuclease assay (such as the TAQMAN PCR method for quantification of PCR), and DNA-chip analysis using the unique nucleic acid sequence SEQ ID Nos:1-181.